[gmx-users] vmd does not display the molecule

[Justin A. Lemkul]

leila karami wrote:
> dear justin
>  
> I transfer gro files from linux to windows through SSH secure shell 
> program. I added 10 Na ions by genion command but in gro file following 
> case is appeared:
>  

If an unrequested Cl is being added, then that is worth investigating.  What was 
your *exact* genion command?

Does the VMD error result in the edited file, or the one that has the additional 
Cl atom?

> 7208Na      Na23127   1.533   2.176   2.687  0.1841 -0.1829 -0.2991
>  7209Na      Na23128   0.179   2.821   0.336 -0.2683 -0.1820  0.5803
>  7210Na      Na23129   2.288   0.458   4.819 -0.1171  0.7612 -0.4903
>  7211Na      Na23130   3.640   1.815   1.138 -0.1083 -0.1591  0.0485
>  7212Na      Na23131   2.183   3.845   1.964 -0.0409 -0.1492  0.6725
>  7213Na      Na23132   3.356   5.216   5.834 -0.2686  0.1059 -0.1660
>  7214Na      Na23133   4.304   2.510   0.809 -0.2994  0.3939  0.7264
>  7215Na      Na23134   4.609   4.931   0.535 -0.2609  0.1315 -0.1767
>  7216Na      Na23135   5.553   6.022   5.152  0.3516 -0.2021  0.2022
>  7217Na      Na23136   5.865   1.114   5.034  0.0442  0.0272  0.3437
> *7218Cl        Cl23137    0.000   0.000   0.000  0.0000   0.0000 0.0000
> *   6.15463   6.21503   6.20117
>  
> I deleted line of        7218Cl        Cl23137    0.000   0.000   
> 0.000  0.0000   0.0000 0.0000
>  
> in top file following case is appeared: 
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> Protein_B           1
> SOL         7117
> Na          10
> Cl          0
>  
> I deleted last line.
>  
> I am using amber03 force field in gromacs program to study interaction 
> of pr-dna.
> 

Then I know that your model is wrong.  You have no N-terminal protonation 
whatsoever!  Think about biology before plowing ahead with computer programs 
that are only capable of doing what you tell them.  Under AMBER, terminal 
residues require a prefix, i.e. NGLY (and CXXX for the C-terminal residues). 
This has been stated many times across this list, and is clearly in the ffamber 
documentation.  Did you perhaps use the -missing flag with pdb2gmx when you got 
an error message?

Perhaps this extra, unwanted, Cl atom is being added by genion because you have 
some bizarre fractional charge on your molecule?

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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